there will not be any permissions problems if they are under the same user account, you can swap the second drive, just make sure you set the 160 gb to slave, the first will always be master.
you can name this new drive whatever you want, it doesn't have to be the same as the one it replaces, as far as a third drive, I don't think there's a port for a third drive. besides that, its simple, drag stuff from old drive to main drive, then install new drive, drag stuff to it.